Gordon Brown and Angela Merkel today agreed to back a new UN conference either in London or Kabul to agree a fresh political course for Afghanistan in the wake of the controversial presidential elections.

Brown flew to Berlin today for talks with Merkel to discuss Afghanistan, underlining the degree to which he fears international co-operation over the war and aid programmes has been too low.

The call for an international UN conference on Afghanistan was first raised by Ari Gaitanis, spokesman for the UN Peacekeeping Department on Friday. But Brown and Merkel may be seeking to extend the conference's remit and status.

The two leaders, together with Nicolas Sarkozy, the French president, will this week write to Ban Ki-moon, the UN secretary general, who would organise the event. Brown said it would be held by the end of the year and would cover security, governance and development.

He and the US are backing a rapid expansion of the Afghan army, as well as an increase in their pay. The Taliban pays families as much as $50 to a family twice the amount paid by the Afghan national army. Brown also explored whether the Germans, present in Afghanistan since 2002, are willing to increase their commitment to training the Afghan army and police. He has highlighted a larger Afghan army as a prerequisite for beating back the Taliban.

The plan has been backed by EU foreign ministers who highlighted the degree to which poorly coordinated aid to Afghanistan worth more than £8bn from the EU alone was being swallowed by a corrupt government.

The conference is not likely to be held until the spring by which time it is hoped that a clear outcome from the presidential elections will have emerged.

With two thirds of votes counted, President Karzai has secured nearly 47% of the vote and since most of the uncounted votes remain in Karzai's Pashtun strongholds it is likely he will win 50% of the vote required to win without a second round. Results from more than 400 stations were annulled yesterday due to suspected fraud.

Germany has more than 4,500 troops stationed in the once largely peaceful north of the country, but is now facing an increasingly resurgent Taliban.

The prospect of extra German troops being sent to the country ahead of the German elections on 27 September is slim, but by the spring there will be calls for extra resources to be spent on the country.

No 10 suggested the conference would probably be held at foreign ministers level, but possibly even heads of government.German support for the war is limited and Merkel came under attack from opposition parties over her government's military involvement.

Gregor Gysi, parliamentary head of the radical Left party, criticised the air strike against hijacked tankers ordered by German troops in Kunduz province on Friday. Mr Gysi called the resulting deaths of civilians "unjustified and inexcusable".

Merkel called for a "thorough, quick" Nato-led investigation into the events surrounding a German-ordered airstrike in northern Afghanistan the air strike and whether civilians were killed in the attack.

She said yesterday she would "deeply regret" if any civilians had been killed and insisted the aim of the German mission is to gain the support and trust of the Afghan people.

Brown also travelled to Berlin to win Merkel's support for the maintenance of the internationally coordinated fiscal stimulus for at least another year. Merkel is seen as the potentially single biggest opponent of the continuation of the stimulus when leaders of the G20 meet in Pittsburgh in two weeks time.

Germany has implemented a large stimulus, but not sought to advertise its policy for domestic reasons, Labour ministers believe. Privately, British ministers believe German support for the stimulus helps isolate the Conservative party in their opposition to extra spending now.

The G20 finance ministers agreed over the weekend that the stimulus should be maintained. Their communique was lukewarm on caps on individual bankers' bonuses but leaves open the possibility that regulators will have a say on pay.

Chancellor Alistair Darling said today that it was too soon to discuss an orderly unwinding of the stimulus, but said that the G20 had agreed that "a transparent and credible process for withdrawal of the stimulus" was needed.

Brown said tonight that he wanted the G20 to support "a global compact for durable growth that would start with a charter of economic principles proposed by the German chancellor, to maintain action to secure co-ordination on exit strategies".